Initial commit for including mouse essential gene param

conf/bagel_species.config

@@ -0,0 +1,12 @@
+params {
+    bagel_gene_sets = [
+        human: [
+            core: '/opt2/bagel-2.0-115/CEGv2.txt',
+            noncore: '/opt2/bagel-2.0-115/NEGv1.txt'
+        ],
+        mouse: [
+            core: '/opt2/bagel-2.0-115/CEG_mouse.txt',
+            noncore: '/opt2/bagel-2.0-115/NEG_mouse.txt'
+        ]
+    ]
+}

docs/params.md

@@ -46,13 +46,14 @@ Define where the pipeline should find input data and save output data.
 
 ## crispr options
 
-| Parameter                    | Description   | Type      | Default                       | Required | Hidden |
-| ---------------------------- | ------------- | --------- | ----------------------------- | -------- | ------ |
-| `drugz_remove_genes`         | comma-sep str | `string`  |                               |          |        |
-| `drugz_half_window_size`     |               | `integer` | 500                           |          |        |
-| `bagel_core_essential_genes` |               | `string`  | /opt2/bagel-2.0-115/CEGv2.txt |          |        |
-| `bagel_non_essential_genes`  |               | `string`  | /opt2/bagel-2.0-115/NEGv1.txt |          |        |
-| `bagel_test_columns`         |               | `string`  |                               |          |        |
+| Parameter                    | Description                                                                                | Type      | Default                       | Required | Hidden |
+| ---------------------------- | ------------------------------------------------------------------------------------------ | --------- | ----------------------------- | -------- | ------ |
+| `drugz_remove_genes`         | comma-sep str                                                                              | `string`  |                               |          |        |
+| `drugz_half_window_size`     |                                                                                            | `integer` | 500                           |          |        |
+| `bagel_species`              | Species for BAGEL analysis; determines default essential and non-essential gene set files. | `string`  | human                         |          |        |
+| `bagel_core_essential_genes` |                                                                                            | `string`  | /opt2/bagel-2.0-115/CEGv2.txt |          |        |
+| `bagel_non_essential_genes`  |                                                                                            | `string`  | /opt2/bagel-2.0-115/NEGv1.txt |          |        |
+| `bagel_test_columns`         |                                                                                            | `string`  |                               |          |        |
 
 ## Docker containers
 

modules/local/bagel.nf

@@ -1,4 +1,32 @@
 
+// Nextflow v2 strict parser compliant: Helper method for species-specific gene sets
+def get_bagel_gene_sets(String species) {
+    if (!params.bagel_gene_sets.containsKey(species)) {
+        error("Unsupported bagel_species '${species}'. Supported species: ${params.bagel_gene_sets.keySet().join(', ')}")
+    }
+
+    return params.bagel_gene_sets[species]
+}
+
+// Helper to resolve gene set file paths based on species or explicit params
+def resolve_bagel_genes() {
+    Map genes = get_bagel_gene_sets(params.bagel_species)
+
+    // Allow explicit params to override species defaults
+    String core_genes = params.bagel_core_essential_genes
+    String noncore_genes = params.bagel_non_essential_genes
+
+    // If using default species-based path, apply species-specific path
+    if (core_genes == '/opt2/bagel-2.0-115/CEGv2.txt') {
+        core_genes = genes.core
+    }
+    if (noncore_genes == '/opt2/bagel-2.0-115/NEGv1.txt') {
+        noncore_genes = genes.noncore
+    }
+
+    return [core: core_genes, noncore: noncore_genes]
+}
+
 process FOLD_CHANGE {
     label 'bagel'
     container "${params.container_bagel}"
@@ -39,12 +67,13 @@ process BAYES_FACTOR {
         path("*.bf"), emit: bf
 
     script:
+    def bagel_genes = resolve_bagel_genes()
     """
     BAGEL.py bf \\
       -i ${fold_change} \\
       -o ${fold_change.getBaseName(2)}.bf \\
-      -e ${params.bagel_core_essential_genes} \\
-      -n ${params.bagel_non_essential_genes} \\
+      -e ${bagel_genes.core} \\
+      -n ${bagel_genes.noncore} \\
       -c ${params.bagel_test_columns}
     """
 
@@ -64,12 +93,13 @@ process PRECISION_RECALL {
         path("*.pr"), emit: pr
 
     script:
+    def bagel_genes = resolve_bagel_genes()
     """
     BAGEL.py pr \\
       -i ${bayes_factor} \\
       -o ${bayes_factor.getBaseName(2)}.pr \\
-      -e ${params.bagel_core_essential_genes} \\
-      -n ${params.bagel_non_essential_genes}
+      -e ${bagel_genes.core} \\
+      -n ${bagel_genes.noncore}
     """
 
     stub:

nextflow.config

@@ -33,12 +33,15 @@ params {
     drugz_half_window_size = 500 // same as default in drugZ https://github.com/hart-lab/drugz/blob/eb15d34e4dd172965e618d5bb662c053066da799/drugz.py#L305-L306
 
     bagel_run = true
+    bagel_species = 'human'
     bagel_core_essential_genes = '/opt2/bagel-2.0-115/CEGv2.txt' // in Docker container
     bagel_non_essential_genes = '/opt2/bagel-2.0-115/NEGv1.txt' // in Docker container
     bagel_test_columns = null
 
 }
 
+
+includeConfig 'conf/bagel_species.config'
 includeConfig 'conf/base.config'
 
 profiles {

nextflow_schema.json

@@ -136,6 +136,12 @@
                     "type": "integer",
                     "default": 500
                 },
+                "bagel_species": {
+                    "type": "string",
+                    "default": "human",
+                    "enum": ["human", "mouse"],
+                    "description": "Species for BAGEL analysis; determines default essential and non-essential gene set files."
+                },
                 "bagel_core_essential_genes": {
                     "type": "string",
                     "default": "/opt2/bagel-2.0-115/CEGv2.txt",